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Old 07-19-2011, 02:05 PM   #3
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Location: US

Join Date: Jan 2009
Posts: 392

Not sure if this is what you want, but a few months back I wrote a very simple perl script (probably not very good, I'm a biologist not a programmer, so my scripts tend to be brute force approaches) that will take a sam file and spit out the names of the reads that map more than once and how many times they mapped.

Now I can't even remember what I was using it for, but maybe it will help you get to where you need.
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Last edited by chadn737; 07-19-2011 at 02:21 PM.
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